@article{shaw10science,
  author = "David E. Shaw and Paul Maragakis and Kresten Lindorff-Larsen and
  Stefano Piana and Ron O. Dror and Michael P. Eastwood and Joseph A. Bank
  and John M. Jumper and John K. Salmon and Yibing Shan and Willy Wriggers",
  issn = "1095-9203",
  journal = "Science",
  number = "6002",
  pages = "341--346",
  title = "Atomic-Level Characterization of the Structural Dynamics of
  Proteins",
  url = {http://dx.doi.org/10.1126/science.1187409},
  volume = 330,
  day = 15,
  month = oct,
  year = 2010
}

@article{greengard87jcp,
  author = "L. Greengard and V. Rokhlin",
  title = "A fast algorithm for particle simulations",
  journal = "Journal of Computational Physics",
  volume = "73",
  issue = "2",
  month = dec,
  year = "1987",
  issn = "0021-9991",
  pages = "325--348",
  numpages = "24",
  url = "http://portal.acm.org/citation.cfm?id=36895.36901",
  publisher = "Academic Press Professional, Inc.",
  address = "San Diego, CA, USA",
} 

@article{valiev10cpc,
  author = "M. Valiev and E.J. Bylaska and N. Govind and K. Kowalski and T.P.
  Straatsma and H.J.J. Van Dam and D. Wang and J. Nieplocha and E. Apra and
  T.L. Windus and W.A. de Jong",
  title = "{NWChem}: A comprehensive and scalable open-source solution for
  large scale molecular simulations",
  journal = "Computer Physics Communications",
  volume = "181",
  number = "9",
  pages = "1477 - 1489",
  year = "2010",
  issn = "0010-4655",
  url = "http://www.sciencedirect.com/science/article/B6TJ5-502V6YP-2/2/2d40ddac658b388d1681698f0642d5e5",
}

@article{kale98namd2,
  author = "Laxmikant Kale and Robert Skeel and Milind Bhandarkar and Robert
  Brunner and Attila Gursoy and Neal Krawetz and James Phillips and Aritomo
  Shinozaki and Krishnan Varadarajan and Klaus Schulten",
  title = "{NAMD2}: Greater Scalability for Parallel Molecular Dynamics",
  journal = "Journal of Computational Physics",
  volume = "151",
  number = "1",
  month = may,
  year = "1999",
  issn = "0021-9991",
  pages = "283--312",
  numpages = "30",
  url = "http://portal.acm.org/citation.cfm?id=316641.316654",
  publisher = "Academic Press Professional, Inc.",
  address = "San Diego, CA, USA",
}

@article{hess08jctc,
  title = "{GROMACS} 4: Algorithms for Highly Efficient, Load-Balanced, and
  Scalable Molecular Simulation",
  author = "B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl",
  journal = "Journal of Chemical Theory and Computation",
  month = mar,
  pages = "435--447",
  url = "http://dx.doi.org/10.1021/ct700301q",
  volume = "4",
  number = "3",
  year = "2008"
}

@article{shaw08acm,
  author = "David E. Shaw and Martin M. Deneroff and Ron O. Dror and Jeffrey S.
  Kuskin and Richard H. Larson and John K. Salmon and Cliff Young and Brannon
  Batson and Kevin J. Bowers and Jack C. Chao and Michael P. Eastwood and
  Joseph Gagliardo and J. P. Grossman and C. Richard Ho and Douglas J. Ierardi
  and Istv\'{a}n Kolossv\'{a}ry and John L. Klepeis and Timothy Layman and
  Christine McLeavey and Mark A. Moraes and Rolf Mueller and Edward C. Priest
  and Yibing Shan and Jochen Spengler and Michael Theobald and Brian Towles and
  Stanley C. Wang",
  title = "Anton, a special-purpose machine for molecular dynamics simulation",
  journal = "Communications of ACM",
  issue_date = "July 2008",
  volume = "51",
  number = "7",
  month = "July",
  year = "2008",
  issn = "0001-0782",
  pages = "91--97",
  numpages = "7",
  url = "http://doi.acm.org/10.1145/1364782.1364802",
  publisher = "ACM",
  address = "New York, NY, USA",
} 

@article{freddolino08bj,
  author = "Peter L. Freddolino and Feng Liu and Martin H. Gruebele and
  Klaus Schulten",
  day = "13",
  journal = "Biophysical Journal",
  volume = 94,
  issue = 10,
  month = mar,
  pages = "L75--L77",
  title = "Ten-microsecond MD simulation of a fast-folding WW domain",
  url = "http://dx.doi.org/10.1529/biophysj.108.131565",
  year = 2008
}

@article{alder57jcs,
  author = "B. J. Alder and T. E. Wainwright",
  title = "Phase Transition for a Hard Sphere System",
  journal = "Journal of Chemical Physics",
  volume = 27,
  issue = 5,
  year = 1957,
  url = "http://dx.doi.org/10.1063%2F1.1743957"
}

@article{gibson60phyrev,
  title = "Dynamics of Radiation Damage",
  author = "J. B. Gibson and A. N. Goland and M. Milgram and G.
  H. Vineyard",
  journal = "Physical Review",
  volume = "120",
  number = "4",
  pages = "1229--1253",
  numpages = "24",
  year = 1960,
  month = nov,
  doi = "10.1103/PhysRev.120.1229",
  publisher = "American Physical Society",
  url = "http://prola.aps.org/abstract/PR/v120/i4/p1229_1"
}

@article{rahman64phyrev,
  title = "Correlations in the Motion of Atoms in Liquid Argon",
  author = "Aneesur Rahman",
  journal = "Physical Review",
  volume = "136",
  number = "2A",
  pages = "A405--A411",
  numpages = "6",
  year = "1964",
  month = "Oct",
  doi = "10.1103/PhysRev.136.A405",
  publisher = "American Physical Society",
  url = "http://prola.aps.org/abstract/PR/v136/i2A/pA405_1"
}

@Article{verlet68phyrev,
  title = "Computer ``Experiments'' on Classical Fluids. II. Equilibrium
  Correlation Functions",
  author = "Loup Verlet",
  journal = "Physical Review",
  volume = "165",
  number = "1",
  pages = "201--214",
  numpages = "13",
  year = "1968",
  month = jan,
  doi = "10.1103/PhysRev.165.201",
  publisher = "American Physical Society",
  url = "http://prola.aps.org/abstract/PR/v165/i1/p201_1"
}

@book{haile97mds,
  author = "J.M. Haile",
  title = "Molecular Dynamics Simulation: Elementary Methods",
  year = "1997",
  publisher = "Wiley Professional",
  isbn = "0-471-81966-2"
}

@inproceedings{shaw09sc,
  author = "David E. Shaw and Ron O. Dror and John K. Salmon and J.
  P. Grossman and Kenneth M. Mackenzie and Joseph A. Bank and Cliff Young and
  Martin M. Deneroff and Brannon Batson and Kevin J. Bowers and Edmond Chow 
  and Michael P. Eastwood and Douglas J. Ierardi and John L. Klepeis and
  Jeffrey S. Kuskin and Richard H. Larson and Kresten Lindorff-Larsen and
  Paul Maragakis and Mark A. Moraes and Stefano Piana and Yibing Shan and
  Brian Towles",
  title = "Millisecond-scale molecular dynamics simulations on Anton",
  booktitle = "Proceedings of the Conference on High Performance Computing
  Networking, Storage and Analysis",
  series = "SC '09",
  year = "2009",
  isbn = "978-1-60558-744-8",
  location = "Portland, Oregon",
  pages = "39:1--39:11",
  articleno = "39",
  numpages = "11",
  publisher = "ACM",
  address = "New York, NY, USA",
  url = "http://doi.acm.org/10.1145/1654059.1654099",
} 

@inproceedings{bhatele08ipdps,
  author = "Abhinav Bhatele and Sameer Kumar and Chao Mei and James C.
  Phillips and Gengbin Zheng and Laxmikant V. Kal\'{a}",
  title = "Overcoming Scaling Challenges in Biomolecular Simulations
  across Multiple Platforms",
  booktitle = "Proceedings of IEEE International Symposium on Parallel and
  Distributed Processing",
  series = "IPDPS '08",
  year = 2008,
  month = apr,
  address = "Miami, Florida, USA",
  url = "http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4536317"
}

@inproceedings{bowers06sc,
  author = "Kevin J. Bowers and Edmond Chow and Huafeng Xu and Ron O. Dror 
  and Michael P. Eastwood and Brent A. Gregersen and John L. Klepeis and
  Istvan Kolossvary and Mark A. Moraes and Federico D. Sacerdoti and 
  John K. Salmon and Yibing Shan and David E. Shaw",
  title = "Scalable algorithms for molecular dynamics simulations on commodity
  clusters",
  booktitle = "Proceedings of the 2006 ACM/IEEE conference on Supercomputing",
  series = "SC '06",
  year = "2006",
  isbn = "0-7695-2700-0",
  location = "Tampa, Florida",
  articleno = "84",
  url = "http://doi.acm.org/10.1145/1188455.1188544",
  publisher = "ACM",
  address = "New York, NY, USA",
} 

@inproceedings{skeel99sif,
  author = "Robert D. Skeel",
  title = "Symplectic integration with floating-point arithmetic and other
  approximations",
  booktitle = "Proceedings of the on Numerical Analysis of Hamiltonian
  Differential Equations",
  year = "1999",
  isbn = "0168-9274",
  location = "Golden, Colorado, United States",
  pages = "3--18",
  numpages = "16",
  url = "http://portal.acm.org/citation.cfm?id=308726.308080",
  publisher = "Elsevier North-Holland, Inc.",
  address = "New York, NY, USA",
}

@techreport{furio97primer,
  author = "Furio Ercolessi",
  title = "A Molecular Dynamics Primer",
  institution = "International School for Advanced Studies",
  address = "Trieste, Italy",
  month = jun,
  year = 1997,
  url = "http://www.fisica.uniud.it/~ercolessi/md/md.pdf"
}

@manual{linuxman,
  title = "Linux Man Pages",
}

@manual{chapelspec,
	organization = "Cray Inc.",
  title = "Chapel Language Specification v0.82",
	url =	"http://chapel.cray.com/spec/spec-0.82.pdf",
  month = oct,
	year = 2011 
}

@electronic{desres,
  title  = "{D. E. Shaw Research}",
  url = "http://www.deshawresearch.com/",
  key = "desres"
}

@electronic{univac,
  title = "{UNIVAC}",
  url = "http://en.wikipedia.org/wiki/UNIVAC",
  key = univac
}

@electronic{ibm704,
  title = "{IBM} 704",
  url = "http://en.wikipedia.org/wiki/IBM_704",
  key = ibm704
}

@electronic{cdc3600,
  title = "{CDC} 3600",
  url = "http://en.wikipedia.org/wiki/CDC_3000",
  key = cdc3600 
}
